Source code for qcdb.psiutil

#
#@BEGIN LICENSE
#
# PSI4: an ab initio quantum chemistry software package
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
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# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
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# You should have received a copy of the GNU General Public License along
# with this program; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
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#@END LICENSE
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r"""Stuff stolen from psi. Should import or not as necessary
or some better way. Apologies to the coders.

"""
import sys
import math
import re
import os
import string
from vecutil import *


def _success(label):
    """Function to print a '*label*...PASSED' line to screen.
    Used by :py:func:`util.compare_values` family when functions pass.

    """
    print('\t{0:.<66}PASSED'.format(label))
    sys.stdout.flush()


[docs]def compare_values(expected, computed, digits, label): """Function to compare two values. Prints :py:func:`util.success` when value *computed* matches value *expected* to number of *digits*. Performs a system exit on failure. Used in input files in the test suite. """ if abs(expected - computed) > 10 ** (-digits): print("\t%s: computed value (%f) does not match (%f) to %d digits." % (label, computed, expected, digits)) sys.exit(1) if math.isnan(computed): print("\t%s: computed value (%f) does not match (%f) to %d digits.\n" % (label, computed, expected, digits)) print("\tprobably because the computed value is nan.") sys.exit(1) _success(label)
[docs]def compare_matrices(expected, computed, digits, label): """Function to compare two matrices. Prints :py:func:`util.success` when elements of matrix *computed* match elements of matrix *expected* to number of *digits*. Performs a system exit on failure to match symmetry structure, dimensions, or element values. Used in input files in the test suite. """ rows = len(expected) cols = len(expected[0]) failed = 0 for row in range(rows): for col in range(cols): if abs(expected[row][col] - computed[row][col]) > 10 ** (-digits): print("\t%s: computed value (%s) does not match (%s)." % (label, expected[row][col], computed[row][col])) failed = 1 break if failed: print("The Failed Test Matrices\n") show(computed) print('\n') show(expected) sys.exit(1) _success(label)
[docs]def query_yes_no(question, default=True): """Ask a yes/no question via raw_input() and return their answer. *question* is a string that is presented to the user. *default* is the presumed answer if the user just hits <Enter>. It must be yes (the default), no or None (meaning an answer is required of the user). The return value is one of True or False. """ yes = re.compile(r'^(y|yes|true|on|1)', re.IGNORECASE) no = re.compile(r'^(n|no|false|off|0)', re.IGNORECASE) if default == None: prompt = " [y/n] " elif default == True: prompt = " [Y/n] " elif default == False: prompt = " [y/N] " else: raise ValueError("invalid default answer: '%s'" % default) while True: sys.stdout.write(question + prompt) choice = raw_input().strip().lower() if default is not None and choice == "": return default elif yes.match(choice): return True elif no.match(choice): return False else: sys.stdout.write(" Please respond with 'yes' or 'no'.\n") ## {{{ http://code.activestate.com/recipes/52224/ (r1)
[docs]def search_file(filename, search_path): """Given a search path, find file """ file_found = False paths = string.split(search_path, os.pathsep) for path in paths: if os.path.exists(os.path.join(path, filename)): file_found = True break if file_found: return os.path.abspath(os.path.join(path, filename)) else: return None ## end of http://code.activestate.com/recipes/52224/ }}}